Variant report

Variant	rs2290257
Chromosome Location	chr2:100016713-100016714
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:100015185-100016857	K562	blood:	n/a	n/a
2	POLR2A	chr2:100011630-100017383	K562	blood:	n/a	n/a
3	POLR2A	chr2:100014429-100016824	K562	blood:	n/a	n/a
4	POLR2A	chr2:100016274-100016950	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:100016113-100016936	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr2:100010038-100028424	K562	blood:	n/a	n/a
7	POLR2A	chr2:100016386-100016746	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr2:100011558-100023544	K562	blood:	n/a	n/a
9	POLR2A	chr2:100013856-100017892	HepG2	liver:	n/a	n/a
10	POLR2A	chr2:100016491-100016919	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:100015839..100018219-chr2:100019045..100021443,2	MCF-7	breast:
2	chr2:100004697..100006240-chr2:100015135..100017156,2	K562	blood:
3	chr2:100007416..100010173-chr2:100015934..100018693,2	MCF-7	breast:
4	chr2:100014826..100019014-chr2:100020376..100023136,4	K562	blood:
5	chr2:100015311..100016881-chr2:100105394..100106940,2	MCF-7	breast:
6	chr2:100014765..100017229-chr2:100029923..100032596,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000273306	TF binding region
ENSG00000135945	Chromatin interaction
ENSG00000273306	Chromatin interaction
ENSG00000158417	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1011633	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs10172068	0.85[JPT][hapmap]
rs10172752	0.84[JPT][hapmap]
rs10187843	0.84[JPT][hapmap]
rs1053544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11123775	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11123782	0.85[JPT][hapmap]
rs11123785	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs11123786	0.85[JPT][hapmap]
rs11676581	0.84[JPT][hapmap]
rs11683651	0.85[JPT][hapmap]
rs11686535	0.85[JPT][hapmap]
rs11687870	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs11884686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11887574	0.84[JPT][hapmap]
rs11892441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11899745	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11902994	0.84[JPT][hapmap]
rs12053519	0.89[JPT][hapmap]
rs12233086	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs12233126	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs12464785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12623540	0.85[JPT][hapmap]
rs13014360	0.83[JPT][hapmap]
rs13017871	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs13018274	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs13026997	0.85[JPT][hapmap]
rs1451243	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs1451245	0.89[JPT][hapmap]
rs1584647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1584648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17022433	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17022564	0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs17022629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2200578	0.89[JPT][hapmap]
rs2242036	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs2290255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2290256	0.85[JPT][hapmap]
rs2290261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2309585	0.85[JPT][hapmap]
rs2309617	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28382892	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3087386	0.84[JPT][hapmap]
rs3749087	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs3791212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3792134	0.85[JPT][hapmap]
rs3792135	0.87[JPT][hapmap]
rs3792136	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs3792137	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs3792142	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs3792146	0.84[JPT][hapmap]
rs3792149	0.85[JPT][hapmap]
rs3811555	0.85[JPT][hapmap]
rs3828316	0.85[JPT][hapmap]
rs4143760	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs4535093	0.85[JPT][hapmap]
rs4850901	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs4851200	0.84[JPT][hapmap]
rs4851205	0.85[JPT][hapmap]
rs4851206	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs6542879	0.85[JPT][hapmap]
rs6542880	0.85[JPT][hapmap]
rs6542882	0.85[JPT][hapmap]
rs6708861	0.85[JPT][hapmap]
rs6711977	0.84[JPT][hapmap]
rs6714244	0.84[JPT][hapmap]
rs6715321	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs6727483	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs717454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7561079	0.85[JPT][hapmap]
rs7561616	0.85[JPT][hapmap]
rs7563462	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7567674	0.84[JPT][hapmap]
rs7571202	0.85[JPT][hapmap]
rs7574135	0.85[JPT][hapmap]
rs7579403	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs7580448	0.85[JPT][hapmap]
rs7585019	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs7585721	0.85[JPT][hapmap]
rs7587419	0.85[JPT][hapmap]
rs7593274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap]
rs7594838	0.84[JPT][hapmap]
rs7597141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7601470	0.85[JPT][hapmap]
rs7601730	0.85[JPT][hapmap]
rs769105	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs896248	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs896249	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs959929	0.85[JPT][hapmap]
rs9941566	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv524466	chr2:99952086-100031551	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1014604	chr2:99980851-100097884	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1006625	chr2:99984550-100096371	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2290257	LYG1	cis	Skin Sun Exposed Lower leg	GTEx
rs2290257	LYG1	cis	Adipose Subcutaneous	GTEx
rs2290257	REV1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99999400-100056800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:100001000-100022000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:100004800-100023000	Strong transcription	Primary B cells from cord blood	blood
4	chr2:100004800-100044800	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr2:100005200-100049800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:100005400-100020000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:100005600-100045400	Strong transcription	Primary T cells from cord blood	blood
8	chr2:100005800-100019600	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:100005800-100019600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:100005800-100045200	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr2:100005800-100062600	Strong transcription	Dnd41	blood
12	chr2:100005800-100066000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:100006000-100019000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:100006000-100019200	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:100006000-100019200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr2:100006000-100019600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:100006000-100023400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr2:100006000-100026200	Strong transcription	HUVEC	blood vessel
19	chr2:100006000-100034200	Strong transcription	GM12878-XiMat	blood
20	chr2:100006000-100046400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:100006000-100049600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr2:100006000-100050800	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr2:100006000-100051000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr2:100006000-100081200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr2:100006200-100017800	Strong transcription	Hela-S3	cervix
26	chr2:100006200-100019000	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr2:100006200-100019800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:100006200-100023600	Strong transcription	Fetal Thymus	thymus
29	chr2:100006200-100028600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:100006200-100046400	Strong transcription	Primary B cells from peripheral blood	blood
31	chr2:100006200-100051400	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr2:100006400-100019400	Strong transcription	Osteobl	bone
33	chr2:100006400-100020200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:100006400-100022600	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr2:100006400-100023000	Strong transcription	Primary hematopoietic stem cells	blood
36	chr2:100006400-100034200	Strong transcription	Fetal Brain Female	brain
37	chr2:100006400-100046600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:100006600-100019000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
39	chr2:100006600-100019400	Strong transcription	Fetal Intestine Large	intestine
40	chr2:100006600-100019600	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr2:100006600-100019600	Strong transcription	Duodenum Mucosa	Duodenum
42	chr2:100006600-100020600	Strong transcription	Placenta	Placenta
43	chr2:100006600-100020800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:100006600-100022400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr2:100006600-100023000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:100006600-100023000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:100006600-100023000	Strong transcription	Thymus	Thymus
48	chr2:100006600-100023200	Strong transcription	K562	blood
49	chr2:100006600-100024000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:100006600-100024000	Strong transcription	Sigmoid Colon	Sigmoid Colon

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